5HPJ

Photobacterium profundum alpha-carbonic anhydrase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A High-Resolution Crystal Structure of a Psychrohalophilic alpha-Carbonic Anhydrase from Photobacterium profundum Reveals a Unique Dimer Interface.

Somalinga, V.Buhrman, G.Arun, A.Rose, R.B.Grunden, A.M.

(2016) PLoS ONE 11: e0168022-e0168022

  • DOI: 10.1371/journal.pone.0168022

  • PubMed Abstract: 
  • Bacterial α-carbonic anhydrases (α-CA) are zinc containing metalloenzymes that catalyze the rapid interconversion of CO2 to bicarbonate and a proton. We report the first crystal structure of a pyschrohalophilic α-CA from a deep-sea bacterium, Photoba ...

    Bacterial α-carbonic anhydrases (α-CA) are zinc containing metalloenzymes that catalyze the rapid interconversion of CO2 to bicarbonate and a proton. We report the first crystal structure of a pyschrohalophilic α-CA from a deep-sea bacterium, Photobacterium profundum. Size exclusion chromatography of the purified P. profundum α-CA (PprCA) reveals that the protein is a heterogeneous mix of monomers and dimers. Furthermore, an "in-gel" carbonic anhydrase activity assay, also known as protonography, revealed two distinct bands corresponding to monomeric and dimeric forms of PprCA that are catalytically active. The crystal structure of PprCA was determined in its native form and reveals a highly conserved "knot-topology" that is characteristic of α-CA's. Similar to other bacterial α-CA's, PprCA also crystallized as a dimer. Furthermore, dimer interface analysis revealed the presence of a chloride ion (Cl-) in the interface which is unique to PprCA and has not been observed in any other α-CA's characterized so far. Molecular dynamics simulation and chloride ion occupancy analysis shows 100% occupancy for the Cl- ion in the dimer interface. Zinc coordinating triple histidine residues, substrate binding hydrophobic patch residues, and the hydrophilic proton wire residues are highly conserved in PprCA and are identical to other well-studied α-CA's.


    Organizational Affiliation

    Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase
A
217Photobacterium profundum (strain SS9)Mutation(s): 0 
Gene Names: EBIG1812
Find proteins for Q6LM17 (Photobacterium profundum (strain SS9))
Go to UniProtKB:  Q6LM17
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.139 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 60.461α = 90.00
b = 60.461β = 90.00
c = 95.464γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United States1332341

Revision History 

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2016-12-28
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence